Blueberry degradome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB23598 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We demonstrate that blueberry supplementation led to global changes in the gut microbiome, which could possibly contribute to physiological changes in mice
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Project description:In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population. Bioinformatic analysis has identified 412 conserved miRNAs, which belong to 20 families, and 57 predicted novel miRNAs likely unique to blueberries. Among them, expression profiles of 5 conserved miRNAs were validated by stem loop qRT-PCR. Furthermore, the potential target genes of the abundant conserved and novel miRNAs were predicted and subjected for Gene Ontology (GO) annotation. Enrichment analysis of the GO-represented biological processes and molecular functions revealed that these target genes were involved in a wide range of metabolic and developmental processes. This study is the first report on genome-wide miRNA profile analysis in blueberry and it provides a useful resource for further elucidation of the functional roles of miRNAs during fruit development and ripening.
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Project description:Characterization of WGBS and RNA-seq in blueberry fruits
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Project description:Blueberry is one of the most desirable and nutritious fruits. During fruit development, the blueberry’s organoleptic properties and phytonutrient composition are ever-changing [1]. Blueberry fruit development is typically described in five phases: pads, cups, green, pink, and blue (ripe) [2]. The former two phases are referred to as the initial “expansion”. During expansion, young fruit is generally hard, dark green and distinguishable by size [3]. The latter three phases are referred to as maturation. Green fruit are hard and fully rounded green berries; pink berries are partially pigmented; blue (ripe) berries are fully colored and soft. Fruit maturation has attracted considerable research attention, and typically, the characteristics fruit softening, coloring, and sweetening are assessed [4].
2019-05-13 | PXD011815 | Pride
Project description:Human volunteers (N=143; 98 females and 45 males; aged 18-45 years) consumed one litre of blueberry-apple juice per day for four weeks. Before and after the intervention blood was drawn and lymphocytes were isolated for subsequent RNA isolation. Each participant acted as his own control.
2014-02-01 | GSE41781 | GEO
Project description:To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline. 4 degradome mixed samples, no replicates, but every degradome data consists of two parts data. Please note that every degradome sample has two processed and two raw data files. To have enough data, additional sequencing was performed from each sample library. And each sample raw data was processed separately (tissue_name*degradome.txt) and also combined (all_degradome*.txt).
2017-05-01 | E-GEOD-72903 | biostudies-arrayexpress
Project description:In this study, blueberry transcriptomics and rhizosphere fungal diversity were analyzed by simulated potting method to treat blueberries with Cd stress, and the content of Fe, Mn, Cu, Zn and Cd in each tissue, soil and DGT of blueberries were determined. , Combined with transcriptomics for correlation analysis. A total of 84374 annotated genes were obtained in blueberry roots, stems, leaves and fruits, of which 3370 DEGs were found, and DEGs in the stem accounted for the highest proportion, totaling 2521. The annotation results show that these DEGs are mainly concentrated in a series of metabolic pathways related to signal transduction, defense and pathogenic response. Blueberries transfer excess Cd from the root to the stem for storage. The stem contains the highest Cd content, which is consistent with the transcriptomics analysis results, while the fruit contains the lowest Cd content. Correlation analysis between heavy metal content and transcriptomics results in each tissue was carried out, and a series of genes related to Cd regulation were screened. The blueberry root system relies on mycorrhiza to absorb nutrients in the soil. The intervention of Cd has severely affected the microflora structure of the blueberry rhizosphere soil. Coniochaetaceae, which is extremely tolerant, has gradually become the dominant population.
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